Discovering and Validating Cuproptosis-Associated Marker Genes for Accurate Keloid Diagnosis Through Multiple Machine Learning Models.

Background: Keloid is a common condition characterized by abnormal scarring of the skin, affecting a significant number of individuals worldwide. Objective: The occurrence of keloids may be related to the reduction of cell death. Recently, a new cell death mode that relies on copper ions has been discovered. This study aimed to identify novel cuproptosis-related genes that are associated with keloid diagnosis. Methods: We utilized several gene expression datasets, including GSE44270 and GSE145725 as the training group, and GSE7890, GSE92566, and GSE121618 as the testing group. We integrated machine learning models (SVM, RF, GLM, and XGB) to identify 10 cuproptosis-related genes (CRGs) for keloid diagnosis in the training group. The diagnostic capability of the identified CRGs was validated using independent datasets, RT-qPCR, Western blotting, and IHC analysis. Results: Our study successfully categorized keloid samples into two clusters based on the expression of cuproptosis-related genes. Utilizing WGCNA analysis, we identified 110 candidate genes associated with cuproptosis. Subsequent functional enrichment analysis results revealed that these genes may play a regulatory role in cell growth within keloid tissue through the MAPK pathway. By integrating machine learning models, we identified CRGs that can be used for diagnosing keloid. The diagnostic efficacy of CRGs was confirmed using independent datasets, RT-qPCR, Western blotting, and IHC analysis. GSVA analysis indicated that high expression of CRGs influenced the gene set related to ECM receptor interaction. Conclusion: This study identified 10 cuproptosis-related genes that provide insights into the molecular mechanisms underlying keloid development and may have implications for the development of targeted therapies.

Effects of marginal zinc deficiency on learning and memory ability after birth.

Zinc deficiency during pregnancy and severe zinc deficiency after birth both impaired learning and memory ability, but the effects of marginal zinc deficiency (MZD) after birth on learning and memory are unclear. In the first experiment, 4-week-old male rats were randomly divided into three groups: the marginal zinc-deficient group (MZG, 10 mg kg-1, 1/3 RNI), normal zinc group (NZG, 30 mg kg-1, RNI), and paired zinc group (PZG, 30 mg kg-1). After a 4-week feeding period, the brain weight, brain coefficient, and serum zinc concentration were measured, and hippocampal proteomics analysis was performed. In the second experiment, 4-week-old male rats were fed the same diet for 8 weeks. In addition to the previously mentioned indicators, the Morris water maze results, brain pathology, post-translational modifications (PTMs) of hippocampal proteins, and the concentrations of indicators known to be related to learning and memory were analyzed. In both experiments, compared with those of the NZG, the food intake, body weight and serum zinc of the MZG were significantly decreased, and the brain weight was unchanged, but the brain coefficient was increased. Two hippocampal proteomics analyses and PTM screening showed that MZD did not change the expression and PTM of proteins. The brain pathology, learning, memory and the concentrations of indicators known to be related to learning and memory were not changed by MZD. Our study confirmed that marginal zinc deficiency (10 mg kg-1, 1/3 RNI) had no effect on the learning and memory abilities of rats after birth.

Integrated multi-omics uncovers reliable potential biomarkers and adverse effects of zinc deficiency.

BACKGROUND: Zinc deficiency is a worldwide public health problem. Currently, there are no established biomarkers available for the accurate diagnosis of zinc-deficiency in individuals. Additionally, a comprehensive view of the adverse effects of zinc deficiency is lacking. Our aim was to identify superior biomarkers of zinc deficiency and uncover the adverse effects of zinc deficiency. METHODS: We performed multi-omics analysis using serum proteomics-metabolomics and liver proteomics on zinc-deficient rats to identify candidate biomarkers and reveal the associated adverse effects of zinc deficiency. Secondly, the candidate biomarkers were validated in two zinc-deficient populations and an RCT zinc supplementation trial on a zinc-deficient population. RESULTS: Our integrated multi-omics approach revealed numerous biomarkers (>2000) and glutathione metabolism as the most important changed pathway in zinc deficiency. Three candidate biomarkers from glutathione metabolism were validated in repeated zinc-deficient rats by quantitative analysis. Only glutathione sulfotransferase omega-1 (GSTO1) (among 3 candidate biomarkers) was validated in the two zinc-deficient populations and zinc-supplemented population. Compared with serum zinc, serum GSTO1 yielded a better response to zinc supplementation and a higher correlation coefficient with zinc intake and the AUC value and has the potential for diagnosing zinc deficiency. By integrated multi-omics, we identified both established and novel adverse effects of zinc deficiency. CONCLUSIONS: Our integrated multi-omics analysis revealed more complete information about zinc deficiency; GSTO1 was found to be a reliable potential biomarker for diagnosis of zinc deficiency. This trial is registered at http://www.chictr.org.cn/registry.aspx as ChiCTR1900028162.

Discrimination of heating and frying vegetable oils based on UPLC/Q-TOF MSMS and chemometrics.

Fried foods have potential adverse effects on health. However, the compounds produced during the process of frying in different vegetable oils are unknown. In this work, ultra performance liquid chromatography (UPLC), quadrupole time-of-flight mass spectrometry (Q-TOF MSMS) and chemical pattern recognition analysis was first conducted to analyze the changes in compounds in 8 different vegetable oils before and after thin-layer heating (without food) and to reveal the potential markers of oil used for deep-frying food. Then, these markers were validated in used frying oil. Our results of principal component analysis (PCA), partial least-squares discriminant analysis (PLS-DA) indicated that both thin-layer heating and deep-frying significantly change the compounds of vegetable oils. Thirty-six of the markers associated with thin-layer heating from the 8 different oils were identified in used frying oils and can be used as common markers of oil used for deep-frying. Additionally, 22 markers detected in individual vegetable oils provided unique markers of used frying oils. These markers can be used to distinguish used frying oil and have the potential to reveal the associated physiological harm.

Serum biomarkers of the calcium-deficient rats identified by metabolomics based on UPLC/Q-TOF MS/MS.

BACKGROUND: We previously identified the urinary biomarkers to diagnose calcium deficiency and nutritional rickets by ultra-performance liquid chromatography/quadrupole time-of-flight tandem mass spectrometry (UPLC/Q-TOF MS/MS). To find biomarkers of calcium deficiency and further confirm these biomarkers in serum, we performed serum metabolomics analysis of calcium-deficient rats. METHODS: A calcium-deficient rat model was established with a low-calcium diet for 12 weeks. Serum metabolomics based UPLC/Q-TOF MS/MS and multivariate statistical analysis was performed to identify the alterations in metabolites associated with calcium deficiency in rats. RESULTS: Bone mineral density, serum parathyroid hormone and alkaline phosphatase were significantly decreased in the low-calcium diet group (LCG) compared to the normal calcium diet group (NCG). Serum metabolic-profiling analysis could definitively distinguish between the LCG and NCG and identified 24 calcium-deficient biomarkers. Three metabolites (indoxyl sulfate, phosphate, and taurine) of the 24 biomarkers were found in our previous urinary metabolomics study of rats with a calcium deficiency and nutritional rickets. The areas under the curve (AUCs) of these three biomarkers were greater than 0.8, and the combination of any two biomarkers was higher than 0.95. CONCLUSION: Dietary calcium deficiency induced the alterations of metabolites in the serum of rats, and the three identified biomarkers had relatively high diagnostic values for calcium deficiency in rats.

The effects of zinc deficiency on homeostasis of twelve minerals and trace elements in the serum, feces, urine and liver of rats.

BACKGROUND: Zinc deficiency can change the concentrations of minerals and trace elements in the body. However, previous studies still had many limitations. OBJECTIVE: To reveal the effects of zinc deficiency on homeostasis of 16 minerals and trace elements. METHODS: Forty-five rats were divided randomly into three groups: normal zinc diet (30 mg/kg), low zinc diet (10 mg/kg), and pair-fed diet(30 mg/kg). The concentrations of 16 minerals and trace elements in serum, feces, urine, and liver were measured by inductively coupled plasma mass spectrometry. The excretion of 16 elements in urine and feces were calculated and compared. RESULTS: Zinc-deficient rats exhibited significant changes in up to 12 minerals and trace elements. The low zinc diet induced decreased excretion of zinc and concentrations of zinc in serum, feces, urine, and liver. Zinc deficiency increased feces concentrations of Mg, Cu, Se, K, Ag, Fe and Mn; decreased the concentrations of Mg, Cu, Se, K in liver and urine, and a diminished amount of Ag was observed in serum. Decreased urinary concentrations of Zn Ca, Mg, Cu, Se, K, Na, As and Cr, suggested that zinc-deficient rats increased the 9 elements' renal reabsorption. Decreased concentrations of Ca in liver, urine, and feces, decreased excretion in urine and feces and increased serum total Ca suggested that zinc deficiency increased the redistribution of Ca in serum or other tissues. Zinc deficiency increased excretion of Cu, Se, Fe; and decreased the excretion of other 8 elements except for Ag. CONCLUSIONS: Zinc deficiency changed the excretion, reabsorption and redistribution of 12 minerals and trace elements in rats. Our findings are the first to show that zinc deficiency alters the concentrations of Ag, Cr, and As. SUPPLEMENTARY INFORMATION: Supplementary information accompanies this paper at 10.1186/s12986-019-0395-y.